Table 1 List of all features.
From: Identifying essential genes in bacterial metabolic networks with machine learning methods
Short form | Explanation |
|---|---|
Topology features | |
a) Deviation | |
RUP | Reachable/Unreachable Products (RUP): equals one if all products could be produced when blocking the reaction, otherwise zero |
PUP | Percentage of Unreachable Products (PUP): the percentage of products which cannot be produced when blocking the reaction |
ND | Number of Deviations (ND) |
APL | Average Path Length (APL): the average path length of the deviations |
LSP | Length of the Shortest Path (LSP): the length of the shortest path of the deviations |
b) Local topology | |
NS | Number of Substrates (NS) |
NP | Number of Products (NP) |
NNR | Number of Neighboring Reactions (NNR) |
NNNR | Number of Neighbors of Neighboring Reactions (NNNR) |
CCV | Clustering Coefficient Value (CCV): clustering coefficient of a reaction |
DIR | Directionality of a reaction (DIR) |
c) Choke points and load scores | |
CP | Choke Point (CP): a reaction is a choke point or not (Rahman et al, 2006) |
LS | Load Score (LS): load score of a reaction (Rahman et al, 2006) |
d) Damage | |
NDR | Number of Damaged Reactions (NDR) (Lemke et al, 2004) |
NDC | Number of Damaged Compounds (NDC) (Lemke et al, 2004) |
NDRD | Number of Damaged Reactions having no Deviations (NDRD): the number of damaged reactions that have no other alternative paths to be reached after blocking a reaction |
NDCD | Number of Damaged Compounds having no Deviations (NDCD): the number of damaged compounds that have no other alternative paths to be reached after blocking a reaction |
NDCR | Number of Damaged Choke point Reactions (NDCR) |
NDCC | Number of Damaged Choke point Compounds (NDCC) |
NDCRD | Number of Damaged Choke point Reactions having no Deviations (NDCRD): the number of damaged choke point reactions that have no other alternative paths to be reached after blocking a reaction |
NDCCD | Number of Damaged Choke point Compounds having no Deviations (NDCCD): the number of damaged choke point compounds that have no other alternative paths to be reached after blocking a reaction |
e) Centrality | |
BW | Betweenness centrality |
CN | Closeness centrality |
EC | Eccentricity centrality |
EV | Eigenvector centrality |
Genomic and transcriptomic features | |
f) Homologs | |
NAR | Number of Associated Reactions (NAR): the number of reactions that base on the knocked-out gene |
Hn | Homology at different expectation values: the number of homologous genes with e-value cutoff 10-30,10-20,10-10,10-7,10-5,10-3 (H30, H20, H10, H7, H5, H3) |
g) Gene expression | |
NGSE | Number of Genes having Similar Expression (NGSE): the number of genes that have similar expression (correlation coefficient >0.8) |
MCC | Maximum of Correlation Coefficients (MCC): maximum value of the correlation coefficients for all neighboring genes |
h) Phyletic retention | |
PR | Phyletic Retention (PR): the number of orthologs in the other prokaryotes |
i) Codon usage | |
Nc | Number of codons |
N3s | Base composition at silent sites (T3s, C3s, A3s, G3s) |
glt | The frequency of amino acids glutamine (exemplarily) |